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A Review of Laboratory Biosafety and Infection Prevention and Control Guidelines on the Management of High-Risk Pathogens in Canada
No full textThe safety precautions required for certain pathogens are different in clinical
laboratories and patient-facing healthcare settings, causing confusion for laboratorians
and infection preventionists. The current review aims to summarize information from reputable Government of Canada guidance commonly used in clinical laboratories in Canada,
including the Government of Canada Human Pathogens and Toxins Act and Regulations,
the ePATHogen—Risk Group Database, biosafety directives and advisories, Transportation
of Dangerous Goods Regulations, and the Canadian Biosafety Standard (2022). Guidelines
from the Centers for Disease Control and Prevention’s (CDC) Biosafety in Microbiological and
Biomedical Laboratories (2020), Clinical and Laboratory Standard Institution’s (CLSI) M29
Protection of Laboratory Workers from Occupationally Acquired Infections (2014), and Association of Public Health Laboratories’s Biothreat Agent Bench Cards for the Sentinel Laboratory
(2018) were also used to supplement specific details. In comparison, information regarding
infection prevention and control practices in patient-facing healthcare settings was summarized: Public Health Agency of Canada: Routine Practices and Additional Precautions for
Preventing the Transmission of Infection in Healthcare Settings (2017) and CDC Infection
Control Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents
in Healthcare Settings (2007). Contrasting levels of precautions exist between laboratories
and patient-facing settings, especially for endemic fungi and certain security-sensitive
biological agents. Acknowledging this contrast may facilitate risk communication relative
to the counterparts to minimize the threat and disease effects and ensure public confidence.Medicine, Faculty ofPharmaceutical Sciences, Faculty ofReviewedFacult
Integrated Transcriptomic and Metabolomic Analysis Reveals Tissue-Specific Flavonoid Biosynthesis and MYB-Mediated Regulation of UGT71A1 in Panax quinquefolius
No full textPanax quinquefolius is a globally valued medicinal plant rich in bioactive flavonoids, yet the molecular mechanisms underlying their biosynthesis remain poorly understood. In this study, we integrated transcriptomic and metabolomic analyses to investigate tissue-specific flavonoid accumulation and regulatory networks in roots, leaves, and flowers. Metabolomic profiling identified 141 flavonoid metabolites, with flavones, flavonols, and C-glycosylflavones predominantly enriched in aerial tissues (leaves and flowers), while specific glycosides like tricin 7-O-acetylglucoside showed root-specific accumulation. Transcriptome sequencing revealed 15,551–18,946 DEGs across tissues, and the reliability of the transcriptomic data was validated by qRT-PCR. KEGG and GO annotation analyses suggested that these DEGs may play a crucial role in the biosynthesis and metabolism of secondary metabolites. From the DEGs, UGTs and MYB TFs were identified and subjected to correlation analysis. Functional validation through in vitro enzymatic assays confirmed that PqUGT71A1 catalyzes apigenin and naringenin glycosylation at the 7-OH position. Additionally, subcellular localization and yeast one-hybrid assays demonstrated that PqMYB7 and PqMYB13 interact with the PqUGT71A1 promoter and activate its expression.. This study unveils the spatial dynamics of flavonoid metabolism in P. quinquefolius and establishes a MYB-UGT regulatory axis, providing critical insights for metabolic engineering and bioactive compound optimization in medicinal plants.Science, Irving K. Barber Faculty of (Okanagan)Non UBCBiology, Department of (Okanagan)ReviewedFacultyResearche
ICD-10 Codes to Identify Adverse Drug Events Associated with Antibiotics in Administrative Data
No full textAntibiotics are among the most used therapeutics in primary care, and while their benefits are clear, the potential harms related to adverse drug events (ADEs) cannot be ignored. We outline the creation of a comprehensive list of diagnostic codes describing antibiotic-associated ADEs resulting in presentations to acute care hospitals. Methods: Previously published ADE codes were used to link BC hospitalizations to prior outpatient antibiotic prescriptions and were restricted based on whether patients received an antibiotic within a month prior to the ADE-related hospitalization. The code list was reviewed by two clinical experts independently for the likelihood of being antibiotic-associated. The inter-rater reliability was calculated using Kappa scores with 95% confidence intervals (CIs). Results: Of the 695 ICD-10 ADE codes with evidence of recent antibiotic administration, 72, 68, and 555 codes were considered likely, possibly, and unlikely antibiotic-associated, respectively. Conclusions: We outline a methodology for developing an ICD-10 code list for antibiotic-associated ADEs severe enough to warrant hospital admission. This will help to improve the use of administrative data to capture antibiotic-associated ADEs.Medicine, Faculty ofPharmaceutical Sciences, Faculty ofEmergency Medicine, Department ofPathology and Laboratory Medicine, Department ofPopulation and Public Health (SPPH), School ofReviewedFacultyResearche
The Effects of Soundscape Interactions on the Restorative Potential of Urban Green Spaces
No full textFrom the perspective of landscape environment and human health, this study
introduces the concept of soundscape from soundscape ecology. Through two experiments
evaluating the restorative properties of soundscapes, it analyzes and compares the differences
in restorative benefits among various sounds in urban green spaces. The study
further explores the effects of single soundscapes and combined soundscape types on
environmental restorative benefits and provides recommendations for creating restorative
soundscapes in urban green spaces. The main findings of this study are as follows:
(1) Sound types significantly influence soundscape restorative benefits, with notable interactions
observed among three single soundscape categories. Significant differences were also
found in the restorative effects of different combined soundscapes. (2) The most restorative
sounds for anthropogenic, biophonic, and geophonic soundscapes are light background
music (1.4193), bird sounds (1.9890), and flowing water sounds (1.2691), respectively. The
least restorative sounds are vehicle noise (−2.6210), conversation sounds (−0.8788), and
thunder sounds (−0.7840). (3) Significant differences exist between the restorative effects
of single and multi-level combined soundscapes. Except for bird sounds, the general
restorative pattern is as follows: two-level combined soundscapes > three-level combined
soundscapes > single soundscapes.Forestry, Faculty ofNon UBCReviewedFacultyResearche
Modelling peaks over thresholds in panel data : a grouped panel generalized Pareto regression model
No full textExtreme Value Theory (EVT) provides probabilistic tools to understand the behaviour of extreme events, making it widely applicable across various fields. When modelling the marginal distributions of the extremes in panel data, one may wish to balance the flexibility to capture the heterogeneity among margins and the efficiency of estimation through a combination of regression technique and assuming a latent group structure among subjects. This group structure facilitating information pooling may not be known a priori and needs to be estimated from data, which may then lead to potential physical interpretations. One existing approach addressing this modelling idea builds on the Block Maxima (BM) method in EVT, which can result in a loss of valuable information. Moreover, similar to the classic k-means clustering method, the current algorithm for estimating group structure is prone to converging to locally optimal solutions. We extend the current approach to a new framework called the grouped panel generalized Pareto regression model, which utilizes the Peaks Over Threshold (POT) method to model excesses over high thresholds, thereby leveraging extreme event information more exhaustively. To account for the conditional dependence structure within clusters of excesses, we introduce a dependence-window-based sandwich estimator for standard error estimation. Taking advantage of the POT method, we develop a new grouping algorithm inspired by hierarchical clustering, which relies on a pre-determined linkage and stopping rule. This algorithm estimates the latent number of groups, the group structure and associated parameters simultaneously, and it demonstrates improved performance in identifying the globally optimal structure and balancing the goodness of fit across subjects under reasonable conditions. The finite-sample performance of our methodology is carefully evaluated through simulation studies, and an application to the river flow data from 31 hydrological stations in Upper Danube river basin is used to illustrate the real-world applicability of our modelling strategy, where the estimation efficiency is notably improved and physically interpretable group structures are identified.Science, Faculty ofStatistics, Department ofGraduat
Memory optimizations for hardware accelerated ray tracing on GPUs
No full textRay tracing is a photorealistic rendering technique that is gaining adoption in real-time graphics applications since the introduction of ray tracing accelerators in modern GPUs. However, current hardware still struggles to meet frame rate demands of real-time ray tracing. The primary bottleneck is acceleration structure traversal, where rays traverse a bounding volume hierarchy (BVH) tree to find the closest intersecting primitive. Irregular memory access patterns and ray divergence contribute to low traversal performance on GPUs and this dissertation addresses these issues through hardware and software co-design. The first work develops Vulkan-Sim, an architectural simulator to study ray tracing performance on GPUs. With the introduction of ray tracing accelerators in GPUs and limited public information, Vulkan-Sim models the ray tracing accelerator in detail and provides a platform for hardware research. We also evaluate two prior ray tracing hardware optimizations, function call coalescing and independent thread scheduling, showing that despite their SIMT efficiency benefits, they provide limited performance benefits for ray tracing workloads. The second work introduces a traversal algorithm leveraging treelets (subtrees of BVH tree), where threads fully traverse a treelet before moving to the next. It also proposes a treelet hardware prefetcher, complimenting the treelet traversal algorithm by fetching treelet nodes in advance, hiding memory latency. This achieves 32.1% speedup over a baseline GPU using a standard DFS traversal order. The third work proposes a treelet-based ray tracing unit that dynamically switches between treelet-stationary and ray-stationary traversal modes to maximize data reuse from the treelet traversal algorithm. We also propose ray virtualization and warp repacking to refill inactive threads with rays, increasing hardware utilization and SIMT efficiency. Results show our design achieves a 95% speedup. The final work presents contributions to scene reconstruction, addressing the non-deterministic nature of neural network training from atomic operation ordering on GPUs. We propose relaxed warp schedulers to only sequence atomic operations within a warp, and atomic buffers to efficiently handle reductions. We also propose a handshake mechanism enforcing ordering of packets arriving from the interconnect across different cores. Our design outperforms state-of-the-art deterministic GPU baseline by 2-4x.Applied Science, Faculty ofElectrical and Computer Engineering, Department ofGraduat
Toward the isolation of pyrazole synthase
No full textThe full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.Science, Faculty ofChemistry, Department ofGraduat
Towards transformative urban sustainability experimentations : possible pathways to affordable housing in Canada
No full textFostering sustainability transitions is an urgent global challenge, and urban Sustainability Experimentations (SEs) have emerged as a critical approach to addressing pressing urban issues through collaboration across various sectors for accelerating urban transitions. Despite their increasing significance, academic literature on SEs in Canada remains in its early stages. In Canada, various SE models and theories have evolved organically, manifested in models such as Social Innovation Labs, Urban Living Labs, Public Sector Innovation Labs, and Demonstrations.
This research addresses How Canadian urban sustainability experimentations (SEs) can become more transformative? To explore this, this research employs a multi-step qualitative case study approach, beginning with a survey of 16 organizations leading SEs across Canada. This step identifies factors contributing to SEs’ diversity, uncovering common challenges and critical elements examined in their processes and broader urban interactions. The second step focuses on two ongoing SEs related to sustainable, affordable housing in Vancouver and Calgary. Data collection included participant interviews, projects and policy document reviews, and observation of decision-making processes. Through in-depth analysis, this research explores the urban dimensions of SEs, their context-specific characteristics within the Canadian setting, and the factors and key dimensions that contribute to their transformative qualities.
The evidence presented in this dissertation highlights that Canadian SEs face significant challenges, including a tendency toward short-term planning, fragmented efforts, uncertainty about long-term impacts, and various contextual and governance factors that hinder their potential to contribute to broader urban transitions. This research provides in-depth discussions, analyses, and conceptual frameworks to identify the key dynamics and dimensions essential for guiding SEs toward broader transformative effects, extending beyond their immediate scope. These factors include but are not limited to shared goal setting, incentivizing risk-taking, connections with broader urban agendas, policies, and other initiatives, cross-disciplinary knowledge co-creation, targeted knowledge dissemination, the confluence of funding programs, research leadership, integrated evaluation in decision-making processes, and attention to power dynamics. The analysis concludes that, despite challenges in navigating uncertainties and evaluating SEs during their processes and limited evidence on their long-term transformative potential, several critical elements can potentially guide practitioners, policymakers, and researchers in steering SEs toward more transformative effects.Applied Science, Faculty ofCommunity and Regional Planning (SCARP), School ofGraduat
Niyam Nritya : a dance of resisting and recreating social norms within Queer South Asian bodies!
No full textThis thesis investigates the relationship between queer South Asians and social norms, arguing that these norms play a critical role in shaping their queer selves, which in turn, impacts their queer authenticity. This investigation is framed through an exploration of relevant scholarship that examines heteronormativity, homonormativity and white normativity as social norms, alongside specific norms within South Asian culture that define their queerness. By applying these theoretical constructs to interviews conducted for this research, the thesis employs a thematic analysis to uncover the lived experience of queer South Asians and draws on inferences about their relationship to social norms. The study illustrates both the adherence to and resistance of social norms, ultimately arguing that queer South Asians actively negotiate with these norms to inform their queer selves and express their queer authenticity.Arts, Faculty ofGender, Race, Sexuality and Social Justice, Institute forGraduat
Development of genetically modified platelets for therapeutic and research applications
No full textThe full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.Medicine, Faculty ofBiochemistry and Molecular Biology, Department ofGraduat